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Found 100 papers, 56 papers with code
Physics-Regularized Multi-Modal Image Assimilation for Brain Tumor Localization
Physical models in the form of partial differential equations represent an important prior for many under-constrained problems.
ISLES 2024: The first longitudinal multimodal multi-center real-world dataset in (sub-)acute stroke
In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome.
ISLES'24: Improving final infarct prediction in ischemic stroke using multimodal imaging and clinical data
This work presents the ISLES'24 challenge, which addresses final post-treatment stroke infarct prediction from pre-interventional acute stroke imaging and clinical data.
BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023
Pediatric central nervous system tumors are the leading cause of cancer-related deaths in children.
FUNAvg: Federated Uncertainty Weighted Averaging for Datasets with Diverse Labels
Federated learning is one popular paradigm to train a joint model in a distributed, privacy-preserving environment.
The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI
Gliomas are the most common malignant primary brain tumors in adults and one of the deadliest types of cancer.
Brain Tumor Segmentation (BraTS) Challenge 2024: Meningioma Radiotherapy Planning Automated Segmentation
The 2024 Brain Tumor Segmentation Meningioma Radiotherapy (BraTS-MEN-RT) challenge aims to advance automated segmentation algorithms using the largest known multi-institutional dataset of radiotherapy planning brain MRIs with expert-annotated target labels for patients with intact or postoperative meningioma that underwent either conventional external beam radiotherapy or stereotactic radiosurgery.
Probabilistic Contrastive Learning with Explicit Concentration on the Hypersphere
Self-supervised contrastive learning has predominantly adopted deterministic methods, which are not suited for environments characterized by uncertainty and noise.
Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge
The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0. 976, 0. 976, and 0. 964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0. 899, 0. 904, and 0. 871, respectively.
The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
DeViDe: Faceted medical knowledge for improved medical vision-language pre-training
These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge.
A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge
We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge.
A foundation model utilizing chest CT volumes and radiology reports for supervised-level zero-shot detection of abnormalities
A major challenge in computational research in 3D medical imaging is the lack of comprehensive datasets.
QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge
The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets.
Simulation-Based Segmentation of Blood Vessels in Cerebral 3D OCTA Images
Segmentation of blood vessels in murine cerebral 3D OCTA images is foundational for in vivo quantitative analysis of the effects of neurovascular disorders, such as stroke or Alzheimer's, on the vascular network.
CT2Rep: Automated Radiology Report Generation for 3D Medical Imaging
Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation.
A Learnable Prior Improves Inverse Tumor Growth Modeling
Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients.
SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation
Training on auto-generated annotations and evaluating on manually corrected test data from the GNC yielded global dice scores of 0. 900 for vertebrae, 0. 960 for intervertebral discs, and 0. 947 for the spinal canal.
MultiMedEval: A Benchmark and a Toolkit for Evaluating Medical Vision-Language Models
We introduce MultiMedEval, an open-source toolkit for fair and reproducible evaluation of large, medical vision-language models (VLM).
Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA
The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology.
Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps
This paper introduces panoptica, a versatile and performance-optimized package designed for computing instance-wise segmentation quality metrics from 2D and 3D segmentation maps.
Personalized Predictions of Glioblastoma Infiltration: Mathematical Models, Physics-Informed Neural Networks and Multimodal Scans
This work proposes a method that uses Physics-Informed Neural Networks (PINNs) to estimate patient-specific parameters of a reaction-diffusion PDE model of GBM growth from a single 3D structural MRI snapshot.
Self-pruning Graph Neural Network for Predicting Inflammatory Disease Activity in Multiple Sclerosis from Brain MR Images
We propose a two-stage MS inflammatory disease activity prediction approach.
MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision
For the medical domain, we present a large collection of anatomical shapes (e. g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems.
Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation
The 3D translation outperformed the 2D approach, resulting in improved Dice scores (0. 80) and anatomically accurate segmentations in a higher resolution than the original MR image.
Inter-Rater Uncertainty Quantification in Medical Image Segmentation via Rater-Specific Bayesian Neural Networks
We introduce a novel Bayesian neural network-based architecture to estimate inter-rater uncertainty in medical image segmentation.
DENTEX: An Abnormal Tooth Detection with Dental Enumeration and Diagnosis Benchmark for Panoramic X-rays
To address these issues, the Dental Enumeration and Diagnosis on Panoramic X-rays Challenge (DENTEX) has been organized in association with the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) in 2023.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)
Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children.
GRAtt-VIS: Gated Residual Attention for Auto Rectifying Video Instance Segmentation
Secondly, we propose a novel inter-instance interaction using gate activation as a mask for self-attention.
Ranked #6 on
Video Instance Segmentation
on YouTube-VIS 2021
(using extra training data)
GenerateCT: Text-Conditional Generation of 3D Chest CT Volumes
GenerateCT, the first approach to generating 3D medical imaging conditioned on free-form medical text prompts, incorporates a text encoder and three key components: a novel causal vision transformer for encoding 3D CT volumes, a text-image transformer for aligning CT and text tokens, and a text-conditional super-resolution diffusion model.
The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn)
In this work, we present the establishment of the Brain MR Image Synthesis Benchmark (BraSyn) in conjunction with the Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2023.
The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma
Meningiomas are the most common primary intracranial tumor in adults and can be associated with significant morbidity and mortality.
Why is the winner the best?
The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning.
Link Prediction for Flow-Driven Spatial Networks
In this work, we focus on link prediction for flow-driven spatial networks, which are embedded in a Euclidean space and relate to physical exchange and transportation processes (e. g., blood flow in vessels or traffic flow in road networks).
Diffusion-Based Hierarchical Multi-Label Object Detection to Analyze Panoramic Dental X-rays
To learn from all three hierarchies jointly, we introduce a novel diffusion-based hierarchical multi-label object detection framework by adapting a diffusion-based method that formulates object detection as a denoising diffusion process from noisy boxes to object boxes.
Understanding metric-related pitfalls in image analysis validation
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice.
ViT-AE++: Improving Vision Transformer Autoencoder for Self-supervised Medical Image Representations
In this paper, we focus on improving ViT-AE (nicknamed ViT-AE++) for a more effective representation of 2D and 3D medical images.
Identifying chromophore fingerprints of brain tumor tissue on hyperspectral imaging using principal component analysis
In this article, we perform a statistical analysis of the brain tumor patients' HSI scans from the HELICoiD dataset with the aim of identifying the correlation between reflectance spectra and absorption spectra of tissue chromophores.
Approaching Peak Ground Truth
Machine learning models are typically evaluated by computing similarity with reference annotations and trained by maximizing similarity with such.
Biomedical image analysis competitions: The state of current participation practice
Of these, 84% were based on standard architectures.
A Domain-specific Perceptual Metric via Contrastive Self-supervised Representation: Applications on Natural and Medical Images
We find that in the natural image domain, CSR behaves on par with the supervised one on several perceptual tests as a metric, and in the medical domain, CSR better quantifies perceptual similarity concerning the experts' ratings.
Topologically faithful image segmentation via induced matching of persistence barcodes
In this work, we propose the first topologically and feature-wise accurate metric and loss function for supervised image segmentation, which we term Betti matching.
Landmark-free Statistical Shape Modeling via Neural Flow Deformations
Statistical shape modeling aims at capturing shape variations of an anatomical structure that occur within a given population.
Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021
This challenge aimed to promote the development of methods for automated detection and segmentation of small and sparse imaging markers of cerebral small vessel disease, namely enlarged perivascular spaces (EPVS) (Task 1), cerebral microbleeds (Task 2) and lacunes of presumed vascular origin (Task 3) while leveraging weak and noisy labels.
Focused Decoding Enables 3D Anatomical Detection by Transformers
To tackle this issue and facilitate the advent of medical Detection Transformers, we propose a novel Detection Transformer for 3D anatomical structure detection, dubbed Focused Decoder.
ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset
The test dataset will be used for model validation only and will not be released to the public.
Metrics reloaded: Recommendations for image analysis validation
The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output.
Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings
To approximate human quality ratings on scarce expert data, we train surrogate quality estimation models.
blob loss: instance imbalance aware loss functions for semantic segmentation
\emph{Blob loss} is designed for semantic segmentation problems where detecting multiple instances matters.
Federated Learning Enables Big Data for Rare Cancer Boundary Detection
Although machine learning (ML) has shown promise in numerous domains, there are concerns about generalizability to out-of-sample data.
Fetal Brain Tissue Annotation and Segmentation Challenge Results
Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context.
A Dempster-Shafer approach to trustworthy AI with application to fetal brain MRI segmentation
Our method automatically discards the voxel-level labeling predicted by the backbone AI that violate expert knowledge and relies on a fallback for those voxels.
Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network
In this work, we present a method for synthetic CT (sCT) generation from zero-echo-time (ZTE) MRI aimed at structural and quantitative accuracies of the image, with a particular focus on the accurate bone density value prediction.
Relationformer: A Unified Framework for Image-to-Graph Generation
We leverage direct set-based object prediction and incorporate the interaction among the objects to learn an object-relation representation jointly.
QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation.
The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients
Registration of longitudinal brain MRI scans containing pathologies is challenging due to dramatic changes in tissue appearance.
FedCostWAvg: A new averaging for better Federated Learning
We propose a simple new aggregation strategy for federated learning that won the MICCAI Federated Tumor Segmentation Challenge 2021 (FETS), the first ever challenge on Federated Learning in the Machine Learning community.
Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling
Current treatment planning of patients diagnosed with a brain tumor, such as glioma, could significantly benefit by accessing the spatial distribution of tumor cell concentration.
The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification
The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions (MICCAI) society.
The Medical Segmentation Decathlon
Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem.
The Federated Tumor Segmentation (FeTS) Challenge
The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i. e. on data from institutional distributions that were not part of the training datasets.
Common Limitations of Image Processing Metrics: A Picture Story
While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.
Differentiable Deconvolution for Improved Stroke Perfusion Analysis
We show that our approach is able to generate AIFs without any manual annotation, and hence avoiding manual rater's influences.
Are we using appropriate segmentation metrics? Identifying correlates of human expert perception for CNN training beyond rolling the DICE coefficient
It is often unclear how to optimize abstract metrics, such as human expert perception, in convolutional neural network (CNN) training.